rs431270

Variant names:

• chr19-23286164-A-C
• rs431270

Your query was ambiguous. Multiple possible variants found:

• chr19-23286164-A-C
• chr19-23286164-A-T

Variant summary

Our verdict is Benign. Variant got -12 ACMG points: 0P and 12B. BP4_Strong BA1

The variant allele was found at a frequency of 0.458 in 151,864 control chromosomes in the GnomAD database, including 18,088 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.46 (18088 hom., cov: 32)
• Consequence: Unknown
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -1.41

ACMG classification

Verdict is Benign. Variant got -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-1.03).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.822 is higher than 0.05.

Transcripts

RefSeq

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	MANE	Protein	UniProt

Ensembl

Gene	Transcript	HGVSc	HGVSp	Effect	Exon rank	TSL	MANE	Protein	Appris	UniProt

Frequencies

GnomAD3 genomes AF: 0.458 AC: 69441 AN: 151746 Hom.: 18033 Cov.: 32

Gnomad AFR AF: 0.671

Gnomad AMI AF: 0.315

Gnomad AMR AF: 0.460

Gnomad ASJ AF: 0.366

Gnomad EAS AF: 0.843

Gnomad SAS AF: 0.464

Gnomad FIN AF: 0.324

Gnomad MID AF: 0.382

Gnomad NFE AF: 0.327

Gnomad OTH AF: 0.410

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.458 AC: 69556 AN: 151864 Hom.: 18088 Cov.: 32 AF XY: 0.459 AC XY: 34038 AN XY: 74236

Gnomad4 AFR AF: 0.672

Gnomad4 AMR AF: 0.460

Gnomad4 ASJ AF: 0.366

Gnomad4 EAS AF: 0.843

Gnomad4 SAS AF: 0.464

Gnomad4 FIN AF: 0.324

Gnomad4 NFE AF: 0.327

Gnomad4 OTH AF: 0.412

Alfa AF: 0.364 Hom.: 10327

Bravo AF: 0.477

Asia WGS AF: 0.610 AC: 2123 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.3

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-1.0
CADD	Benign	2.3
DANN	Benign	0.27

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

Publications

LitVar

Other links and lift over

dbSNP: rs431270; hg19: chr19-23468966;